The river originates at Khagrachharhi's Halda Valley and enters Chittagong through Fatikchharhi in the north-east.
In 2011, the government constructed a dam on the river at Fatikchharhi to facilitate irrigation.
A similar dam was built on the river's Harualchharhi Canal the following year.
But the dams have reduced water flow in the once vibrant river leading to a rise in salinity, said Chittagong University teacher Manjurul Kibria.
"Saline water enters Halda from the Karnaphuli River during high tides," said the zoology department associate professor.
This has resulted in a drop in production of fish eggs.
A chemist at Chittagong WASA said the Halda's tolerable salinity limit was 600 parts per million.
"We found it to be three times higher in November, December last year and January this year," he said, preferring anonymity.
Salinity and right temperature are necessary for the mother fish to lay eggs.
"It's a delicate balance. A slight change in salinity or temperature hampers fish-egg production," said Kibria, who leads a movement for conserving the river.
He said the dwindling production over the past two years is evidence of that.
Moreover, there have been reports of illegal poaching of mother fishes.
Locals claim the fishes are mainly hunted at Rauzan and Hathazari Upazilas during the night.
Chittagong district fisheries officer Provati Deb said the fishes are hunted in areas along the Kaptai dam, which is not under her project.